Brownian dynamics simulations on CPU and GPU with BD_BOX

Długosz, Maciej; Zieliński, Paweł; Trylska, Joanna

doi:10.1002/jcc.21847

Cited by 47 publications

(49 citation statements)

References 58 publications

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“…However, these calculations can take a significant amount of computational resources, especially when hundreds of thousands of simulations or long single simulations are required for sufficient statistical sampling. Some methods use multiple diffusing particles, [21][22][23] and some consider only one moving particle at a time. [17][18][19][20] Whereas Brownian dynamics focuses on the movement of particular particles, the continuum methods can be used to study overall diffusion patterns exhibited by a collection of particles.…”

Section: Introductionmentioning

confidence: 99%

“…[17][18][19][20][21][22] This method has the benefit of providing trajectories of the diffusing particle as it interacts with a target, and this method can be especially useful for looking at protein-protein interactions. However, since the usefulness of this method is based on statistics, many simulations must be run in order to have meaningful results.…”

Section: Introductionmentioning

confidence: 99%

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Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions

Bauler

Huber

McCammon

2012

The Journal of Chemical Physics

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Diffusion is often the rate determining step in many biological processes. Currently, the two main computational methods for studying diffusion are stochastic methods, such as Brownian dynamics, and continuum methods, such as the finite element method. This paper proposes a new hybrid diffusion method that couples the strengths of each of these two methods. The method is derived for a general multidimensional system, and is presented using a basic test case for 1D linear and radially symmetric diffusion systems.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions

Bauler

Huber

McCammon

2012

The Journal of Chemical Physics

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“…In particular, we have found the explicit form of the dipolar components of the mobility matrix (3.6) and (3.9), needed in order to track the dynamics of the system under shear flow. Additionally, we have derived expressions for all the components of the mobility matrix for overlapping particles, which is needed in both the Brownian dynamics simulations (Długosz, Zieliński & Trylska 2011;Geyer 2011) as well as in the calculation of hydrodynamic properties with bead models (Byron 1997;Zipper & Durchschlag 1997;de la Torre et al 2000). By construction, the N-particle mobility matrix obtained using (2.8) is positive definite and all the hydrodynamic tensors have the correct limiting behaviour for touching spheres and for complete overlap, with one sphere immersed in another.…”

Section: Discussionmentioning

confidence: 99%

Rotne–Prager–Yamakawa approximation for different-sized particles in application to macromolecular bead models

et al. 2014

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The Rotne-Prager-Yamakawa (RPY) approximation is a commonly used approach to model the hydrodynamic interactions between small spherical particles suspended in a viscous fluid at a low Reynolds number. However, when the particles overlap, the RPY tensors lose their positive definiteness, which leads to numerical problems in the Brownian dynamics simulations as well as errors in calculations of the hydrodynamic properties of rigid macromolecules using bead modelling. These problems can be avoided by using regularizing corrections to the RPY tensors; so far, however, these corrections have only been derived for equal-sized particles. Here we show how to generalize the RPY approach to the case of overlapping spherical particles of different radii and present the complete set of mobility matrices for such a system. In contrast to previous ad hoc approaches, our method relies on the direct integration of force densities over the sphere surfaces and thus automatically provides the correct limiting behaviour of the mobilities for the touching spheres and for a complete overlap, with one sphere immersed in the other one. This approach can then be used to calculate hydrodynamic properties of complex macromolecules using bead models with overlapping, different-sized beads, which we illustrate with an example.

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“…The MD packages discussed above [42]–[46], [66], [68] as well as many BD [69] and reaction-diffusion packages [28], [29], [70]–[72] provide parallel computation. The ReaDDy implementation presented in this work is a single-core CPU version, intended to be a reference implementation of our design.…”

Section: Readdy Softwarementioning

confidence: 99%

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

2013

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We introduce the software package ReaDDy for simulation of detailed spatiotemporal mechanisms of dynamical processes in the cell, based on reaction-diffusion dynamics with particle resolution. In contrast to other particle-based reaction kinetics programs, ReaDDy supports particle interaction potentials. This permits effects such as space exclusion, molecular crowding and aggregation to be modeled. The biomolecules simulated can be represented as a sphere, or as a more complex geometry such as a domain structure or polymer chain. ReaDDy bridges the gap between small-scale but highly detailed molecular dynamics or Brownian dynamics simulations and large-scale but little-detailed reaction kinetics simulations. ReaDDy has a modular design that enables the exchange of the computing core by efficient platform-specific implementations or dynamical models that are different from Brownian dynamics.

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Brownian dynamics simulations on CPU and GPU with BD_BOX

Cited by 47 publications

References 58 publications

Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions

Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions

Rotne–Prager–Yamakawa approximation for different-sized particles in application to macromolecular bead models

ReaDDy - A Software for Particle-Based Reaction-Diffusion Dynamics in Crowded Cellular Environments

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